AMR/man/microorganisms.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/data.R
\docType{data}
\name{microorganisms}
\alias{microorganisms}
\title{Data set with human pathogenic microorganisms}
\format{A \code{\link{tibble}} with 2,642 observations and 14 variables:
\describe{
  \item{\code{mo}}{ID of microorganism}
  \item{\code{bactsys}}{Bactsyscode of microorganism}
  \item{\code{genus}}{Genus name of microorganism, like \code{"Echerichia"}}
  \item{\code{species}}{Species name of microorganism, like \code{"coli"}}
  \item{\code{subspecies}}{Subspecies name of bio-/serovar of microorganism, like \code{"EHEC"}}
  \item{\code{fullname}}{Full name, like \code{"Echerichia coli (EHEC)"}}
  \item{\code{gramstain}}{Gram of microorganism, like \code{"Negative rods"}}
  \item{\code{aerobic}}{Logical whether bacteria is aerobic}
  \item{\code{family}}{Taxonomic family of the microorganism as found in ITIS, see Source}
  \item{\code{order}}{Taxonomic order of the microorganism as found in ITIS, see Source}
  \item{\code{class}}{Taxonomic class of the microorganism as found in ITIS, see Source}
  \item{\code{phylum}}{Taxonomic phylum of the microorganism as found in ITIS, see Source}
  \item{\code{type}}{Type of microorganism, like \code{"Bacteria"} and \code{"Fungus/yeast"}}
  \item{\code{prevalence}}{A rounded integer based on prevalence of the microorganism. Used internally by \code{\link{as.mo}}, otherwise quite meaningless.}
}}
\source{
Integrated Taxonomic Information System (ITIS) on-line database, \url{https://www.itis.gov}.
}
\usage{
microorganisms
}
\description{
A data set containing (potential) human pathogenic microorganisms. MO codes can be looked up using \code{\link{guess_mo}}.
}
\seealso{
\code{\link{guess_mo}} \code{\link{antibiotics}} \code{\link{microorganisms.umcg}}
}
\keyword{datasets}